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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/simple__methods_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/aln_score/simple_methods.cpp Source File

40 #include <wx/checkbox.h> 41 #include "wx/valgen.h" 51  if

(base == consensus)

58  return

base == consensus;

60  return

base ==

'C'

|| base ==

'A'

;

62  return

base ==

'G'

|| base ==

'A'

;

64  return

base ==

'G'

|| base ==

'C'

;

66  return

base ==

'G'

|| base ==

'C'

|| base ==

'A'

;

68  return

base ==

'T'

|| base ==

'A'

;

70  return

base ==

'T'

|| base ==

'C'

;

72  return

base ==

'T'

|| base ==

'C'

|| base ==

'A'

;

74  return

base ==

'T'

|| base ==

'G'

;

76  return

base ==

'T'

|| base ==

'G'

|| base ==

'A'

;

78  return

base ==

'T'

|| base ==

'G'

|| base ==

'C'

;

80  return

base ==

'T'

|| base ==

'G'

|| base ==

'C'

|| base ==

'A'

;

82  return

base == consensus;

89  if

(consensus == residue)

93  return

residue ==

'N'

|| residue ==

'D'

;

95  return

residue ==

'I'

|| residue ==

'L'

;

97  return

residue ==

'Q'

|| residue ==

'E'

;

99  return

consensus == residue;

108  switch

(align_type) {

109  case

IAlnExplorer::EAlignType::fDNA:

117  case

IAlnExplorer::EAlignType::fMixed:

133

: m_Space(0), m_Gap(0)

148

: m_Space(0), m_Gap(0)

167

: m_Worst(

orig

.m_Worst),

168

m_Best(

orig

.m_Best),

169

m_Space(

orig

.m_Space),

210  return "Frequency-Based Difference"

;

213 #define SIMPLE_DESCR "This is a column-based method that assigns scores \ 214 to residues in a column based on their representation in the column's frequency \ 215 profile. Residues that occur infrequently are highlighted darkly; columns \ 216 that contain any degree of mismatch will alsobe highlighted." 254  size_t

total =

column

.size() - space_n;

258  for

(

size_t i

= 0;

i

<

column

.size();

i

++ ) {

304  int

index = (

int

) floor(score *

size

);

338

DECLARE_EVENT_TABLE()

344  void OnApply

( wxCommandEvent& event );

358

m_Method(method), m_GradPanel()

374

wxBoxSizer* itemBoxSizer1 =

new

wxBoxSizer(wxVERTICAL);

375

this->SetSizer(itemBoxSizer1);

385

itemBoxSizer1->Add(

m_GradPanel

, 1, wxGROW|wxALL, 5);

387

wxCheckBox* itemCheckBox1 =

new

wxCheckBox(

this

,

wxID_ANY

,

_

(

"Ignore Empty Space"

));

388

itemCheckBox1->SetValidator(wxGenericValidator(&

m_Space

));

389

itemBoxSizer1->Add(itemCheckBox1, 0, wxALIGN_LEFT|wxALL, 5);

391

wxCheckBox* itemCheckBox2 =

new

wxCheckBox(

this

,

wxID_ANY

,

_

(

"Ignore Gaps"

));

392

itemCheckBox2->SetValidator(wxGenericValidator(&

m_Gap

));

393

itemBoxSizer1->Add(itemCheckBox2, 0, wxALIGN_LEFT|wxALL, 5);

424

m_UndefColor(0.8f, 0.8f, 1.0f),

432

m_UndefColor(

orig

.m_UndefColor)

445  return "Show Differences"

;

449 #define SNP_DESCR "This method highlights differences observed from the master \ 450 sequence in an alignment. In order to see any coloration with this scheme, \ 451 you must select a master sequence. You can adjust the master sequence \ 452 on the fly and display differences by selecting a new master from the context menu."

;

461 const static float kSNP

= 0.0f;

479

fill(scores.begin(), scores.end(),

kUndef

);

481  for

(

size_t i

= 0;

i

<

column

.size();

i

++ ) {

548

DECLARE_EVENT_TABLE()

554  void OnApply

( wxCommandEvent& event );

583

wxBoxSizer* itemBoxSizer1 =

new

wxBoxSizer(wxVERTICAL);

584

this->SetSizer(itemBoxSizer1);

586

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxHORIZONTAL);

588

wxColourPickerCtrl* itemColorPicker1 =

new

wxColourPickerCtrl(

this

,

wxID_ANY

);

590

itemBoxSizer2->Add(itemColorPicker1, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

591

itemBoxSizer2->Add(

new

wxStaticText(

this

, wxID_STATIC,

_

(

"Neutral (no master specified)"

)),

592

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

593

itemBoxSizer1->Add(itemBoxSizer2, 0, wxALIGN_LEFT|wxALL, 0);

595

itemBoxSizer2 =

new

wxBoxSizer(wxHORIZONTAL);

596

wxColourPickerCtrl* itemColorPicker2 =

new

wxColourPickerCtrl(

this

,

wxID_ANY

);

598

itemBoxSizer2->Add(itemColorPicker2, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

599

itemBoxSizer2->Add(

new

wxStaticText(

this

, wxID_STATIC,

_

(

"SNP"

)),

600

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

601

itemBoxSizer1->Add(itemBoxSizer2, 0, wxALIGN_LEFT|wxALL, 0);

603

itemBoxSizer2 =

new

wxBoxSizer(wxHORIZONTAL);

604

wxColourPickerCtrl* itemColorPicker3 =

new

wxColourPickerCtrl(

this

,

wxID_ANY

);

606

itemBoxSizer2->Add(itemColorPicker3, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

607

itemBoxSizer2->Add(

new

wxStaticText(

this

, wxID_STATIC,

_

(

"Normal"

)),

608

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

609

itemBoxSizer1->Add(itemBoxSizer2, 0, wxALIGN_LEFT|wxALL, 0);

611

wxCheckBox* itemCheckBox1 =

new

wxCheckBox(

this

,

wxID_ANY

,

_

(

"Ignore Empty Space"

));

612

itemCheckBox1->SetValidator(wxGenericValidator(&

m_Space

));

613

itemBoxSizer1->Add(itemCheckBox1, 0, wxALIGN_LEFT|wxALL, 5);

615

wxCheckBox* itemCheckBox2 =

new

wxCheckBox(

this

,

wxID_ANY

,

_

(

"Ignore Gaps"

));

616

itemCheckBox2->SetValidator(wxGenericValidator(&

m_Gap

));

617

itemBoxSizer1->Add(itemCheckBox2, 0, wxALIGN_LEFT|wxALL, 5);

664  return "Test Sequence-based"

;

696  size_t

color_index = 0;

698  switch

(

buf

[

i

]) {

739  size_t

index = (size_t) score;

755

wxUnusedVar(

color

);

793

: m_ColumnCount(0), m_SequenceLevel(

orig

.m_SequenceLevel)

795  for

(

auto i

= 0;

i

< EColors::eLast; ++

i

)

809  return "Nonsynonymous substitutions"

;

813 Note: nonsynonymous substitution coloring is available only for CDS alignments. 814 Any sequence in alignment or pre-calculated consensus with only ACGT letters can be set as a master.)foo"; 833

fill(scores.begin(), scores.end(), -1.);

835  for

(

size_t i

= 0;

i

<

column

.size();

i

++) {

836  bool

same = (

column

[

i

] == cons);

867  int

index = (

int

) floor(score *

size

);

void GetParams(stParams &params) const

CNonSynonymousScoringMethod - implementation of IScoringMethod.

CRgbaGradColorTable m_ColorTable

virtual string GetName() const override

returns unique name of the method that is used in UI to identify it

virtual int GetType() const override

returns combination of EAlignType flags defining types of alignments that can be colored with this me...

virtual int GetSupportedColorTypes() const override

returns a combination of EColorType flags

virtual string GetDescription() const override

returns a detailed description of the method that is used in UI

virtual void CalculateScores(char cons, const string &column, TScore &col_score, TScoreVector &scores) override

virtual const CRgbaColor & GetColorForNoScore(EColorType type) const override

Call for display colors when CanCalculateScores returns false.

virtual const CRgbaColor & GetColorForScore(TScore score, EColorType type) const override

returns a color corresponding to a given score value.

virtual ~CNonSynonymousScoringMethod()

CNonSynonymousScoringMethod()

CNonSynonymousScoringMethod.

virtual IUITool * Clone() const override

virtual void SetColorForNoScore(EColorType type, const CRgbaColor &color) override

CRgbaColor m_Colors[EColors::eLast]

class CRgbaColor provides a simple abstraction for managing colors.

virtual string GetDescription() const

returns a detailed description of the method that is used in UI

virtual IUITool * Clone() const

virtual int GetSupportedColorTypes() const

returns a combination of EColorType flags

friend class CSNPScoringPanel

virtual bool HasPropertiesPanel() const

returns true if the method supports properties dialog

virtual bool CanCalculateScores(const IScoringAlignment &aln)

Do we have what it takes to calculate scores? e.g. a master row selected?

virtual const CMenuItem * GetMenu()

Returns a pointer to the submenu.

virtual const CRgbaColor & GetColorForNoScore(EColorType type) const

Call for display colors when CanCalculateScores returns false.

virtual const CRgbaColor & GetColorForScore(TScore score, EColorType type) const

returns a color corresponding to a given score value.

virtual void CalculateScores(char cons, const string &column, TScore &col_score, TScoreVector &scores)

CSNPScoringMethod()

CSNPScoringMethod.

virtual wxWindow * CreatePropertiesPanel(wxWindow *parent)

This a factory method that shall produce a CPropertiesPanel representing properties of the method; th...

virtual string GetName() const

returns unique name of the method that is used in UI to identify it

virtual void SetColorForNoScore(EColorType type, const CRgbaColor &color)

void OnApply(wxCommandEvent &event)

CSNPScoringPanel(CSNPScoringMethod &method, wxWindow *parent, wxWindowID id=wxID_ANY)

CSNPScoringMethod & m_Method

CSimpleScoringMethod - trivial implementation of IScoringMethod.

virtual IUITool * Clone() const

virtual void CalculateScores(char cons, const string &column, TScore &col_score, TScoreVector &scores)

friend class CSimpleScoringPanel

CSimpleScoringMethod()

CSimpleScoringMethod.

virtual int GetType() const

returns combination of EAlignType flags defining types of alignments that can be colored with this me...

unique_ptr< CMenuItem > m_Menu

virtual wxWindow * CreatePropertiesPanel(wxWindow *parent)

This a factory method that shall produce a CPropertiesPanel representing properties of the method; th...

CRgbaGradColorTable m_ColorTable

virtual bool CanCalculateScores(const IScoringAlignment &aln)

Do we have what it takes to calculate scores? e.g. a master row selected?

virtual string GetDescription() const

returns a detailed description of the method that is used in UI

virtual bool IsAverageable() const

return "true" if scores could be averaged

virtual const CRgbaColor & GetColorForNoScore(EColorType type) const

Call for display colors when CanCalculateScores returns false.

CRgbaColor m_Worst

combination of EOptions flags

void SetOptions(int options)

virtual void SetColorForNoScore(EColorType type, const CRgbaColor &color)

vector< int > m_vCharCounts

char m_Space

histogramm of characters

virtual string GetName() const

returns unique name of the method that is used in UI to identify it

void CreateColorTable(int size)

virtual const CMenuItem * GetMenu()

Returns a pointer to the submenu.

virtual ~CSimpleScoringMethod()

virtual bool HasPropertiesPanel() const

returns true if the method supports properties dialog

virtual int GetSupportedColorTypes() const

returns a combination of EColorType flags

virtual const CRgbaColor & GetColorForScore(TScore score, EColorType type) const

returns a color corresponding to a given score value.

void OnApply(wxCommandEvent &event)

CSimpleScoringMethod & m_Method

CGradientColorPanel * m_GradPanel

CSimpleScoringPanel(CSimpleScoringMethod &method, wxWindow *parent, wxWindowID id=wxID_ANY)

int GetType() const

returns combination of EAlignType flags defining types of alignments that can be colored with this me...

virtual void CalculateScores(IAlnExplorer::TNumrow row, const IScoringAlignment &aln, TScoreColl &scores)

virtual int GetSupportedColorTypes() const

returns a combination of EColorType flags

CTestSeqBasedMethod()

CTestSeqBasedMethod.

virtual const CRgbaColor & GetColorForScore(TScore score, EColorType type) const

returns a color corresponding to a given score value.

virtual string GetName() const

returns unique name of the method that is used in UI to identify it

virtual string GetDescription() const

returns a detailed description of the method that is used in UI

virtual const CRgbaColor & GetColorForNoScore(IScoringMethod::EColorType type) const

Call for display colors when CanCalculateScores returns false.

CRgbaColor m_NoScoreColor

vector< CRgbaColor > m_vColors

virtual void SetColorForNoScore(IScoringMethod::EColorType type, const CRgbaColor &color)

virtual bool IsAverageable() const

return "true" if scores could be averaged

virtual IUITool * Clone() const

virtual void UpdateSettings(const IScoringAlignment &aln)

Set alignment specifi settings.

std::function< bool(char c, char b)> mf_CompareResidue

char m_AmbiguousResidue

Ambiguous Residue, typically 'N' for nucleotides, 'X' for proteins.

static const int kAmbiguousResidueScore

virtual TSeqPos GetAlnStart() const =0

virtual IAlnExplorer::EAlignType GetAlignType() const =0

virtual TSeqPos GetAlnStop() const =0

virtual string & GetAlnSeqString(IAlnExplorer::TNumrow row, string &buffer, const IAlnExplorer::TSignedRange &aln_range) const =0

vector< TScore > TScoreVector

static const int sm_DefGradientSize

default number of colors in gradient

static const Colors colors

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const char * column

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void SetSize(size_t size)

void FillGradient(const CRgbaColor &start_c, const CRgbaColor &end_c)

initialize the whole table with gradient colors in [start_c, end_c] range

void SetFrom(TSeqPos start)

void Set(float r, float g, float b)

set the color from an Fl_Color

void Lighten(float scale)

void push_back(const attr_type &attr)

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

A callback function used to compare two keys in a database.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

const struct ncbi::grid::netcache::search::fields::SIZE size

static const float kUndef

const string CNONSYNONYMOUS_METHOD_DESCR

static bool s_CompareBases(char consensus, char base)

static bool s_CompareResidues(char consensus, char residue)

static const int kDefGradientSize

static const float kSameBase

#define row(bind, expected)

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